The film explicitly does not answer the question of what happens to a dead person's soul. I would point out, however, that Olga has been dead for two weeks, and Paul has not complained about lacking a soul. He seems to be acutely aware of the situation when he is without a soul, so I assume that Olga's soul, or at least part of it, is still active in him.
1) why they wouldn't take out the poet's soul first (why would Paul want to keep it in there in additon)
They are operating under serious time pressure. They have to finish before Sveta wakes up or someone else shows up at the facility. Their priority is to get Paul's soul back into him, and they just don't have time to do it the right way. Part of the time pressure is that they need to be as far away from the facility as possible before Dimitri starts looking for them.
It is perhaps lucky that they don't have time to think about the issue of what to do with Olga's soul. Both Nina and Paul have connected with Olga's soul, and they would not feel good about casting it adrift.
2) why Paul has enough "space" to accommodate two souls yet Nina can't put back her own.
Souls are of all different sizes. Probably, people differ in their capacity for souls. Nina has accumulated a whole mess of fragments (residues), and there may not be room for her original soul in addition to them. (We don't know how long Nina has been transporting souls. Once a month for five years would be a lot of fragments.) We don't have any information about Paul's capacity for carrying souls.
Paul's soul, when he gets it back, is smaller than it originally was. Residues are left in Nina and Sveta. Also, it is possible that it atrophied to some degree in Sveta. Olga's soul is smaller than it originally was. Part of it stayed in Olga, and a residue stayed in Nina.
We are told that when Paul's soul is originally extracted, at least 95% of it was removed. He is tested to determine this, and the implication is that the extraction rate varies. This is all of the information we're given about extraction rates, and it is only one case.
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